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* [svn-r18992] Bug Fix: (ID 1921)Albert Cheng2010-06-113-34/+37
| | | | | | | | | | | | PHDF5 changed to use "mpiexec", instead of mpirun, as the default MPI applications startup command as defined in the MPI-2 definition, section 4.1. Note that only mpich related (using mpicc command) definitions are changed to mpiexec. Other favors like hcc, AIX, champion, are not changed since I don't have a way to verify them yet. Tested: jam and amani, using both current and new mpich. Did not h5committested since this affects PHDF5 configure only.
* [svn-r18987] Description:Frank Baker2010-06-081-0/+6
| | | | Add acknowledgment of LBNL contractual support.
* [svn-r18985] Test feature: (bugs 1919)Albert Cheng2010-06-084-5/+37
| | | | | | | | | | | | | | | | Problem: some launching command like yod (and sometimes mpirun), do not pass back the exit code of the executables back to the shell. It always returns 0 if it can launch the executable. This cause tests that expect non-zero exit code to fail incorrectly. Short term Solution: Added the feature that if $RUNSERIAL_NOEXITCODE is defined, do not test conditions that rely on non-zero exit code. Tests: dove-linux using RUNSERIAL=thgyod to see the failures and using $RUNSERIAL_NOEXITCODE=yes to bypass the errors. Also h5committested.
* [svn-r18984] Description:Albert Cheng2010-06-071-3/+9
| | | | | | | Fixed exit code (sometimes return code in Main) to follow the HDF5 standards. Tested: Tested in Dove-linux only since change is trivial and has passed in v1.8.
* [svn-r18976] Added comments regarding the -D_POSIX_SOURCE flag including a ↵Larry Knox2010-06-041-1/+12
| | | | | | reference to a discussion of the _POSIX_SOURCE, BSD_SOURCE, and _POSIX_C_SOURCE Macros and their intersaction at http://www.gnu.org/s/libc/manual/html_node/Feature-Test-Macros.html. Comment text only - not tested.
* [svn-r18965] Windows use of VC_EXTRALEAN no longer did anything. It has been ↵Allen Byrne2010-06-035-11/+8
| | | | | | | | replaced by WIN32_LEAN_AND_MEAN macro. This was the cause of a define conflict causing the use of grp1 and grp2 to be replaced with constants in the h5dumpgentest.c file. This also affected the use of the #include <winsock.h> needed by gethostname. The new include: winsock2.h has been added to h5private.h and either removed or updated in the other files. Tested: Windows
* [svn-r18963] Purpose:Mike McGreevy2010-06-032-0/+16
| | | | Add acknowledgments file to top level of hdf5 trunk distribution.
* [svn-r18958] Purpose:Jonathan Kim2010-06-031-12/+12
| | | | | | Fixed Windows compile error. Renamed to use 'gid1' and 'gid2' instead of 'grp1' and 'grp2'. Description: There is variable name confliction with 'grp1' ~ 'grp9' in Windows system. It occurs if H5private.h is included in the code.
* [svn-r18956] Corrected name of external librariesAllen Byrne2010-06-031-2/+2
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* [svn-r18950] Correct version numbers for trunkAllen Byrne2010-06-021-3/+3
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* [svn-r18949] Corrected where the static *.mod files are installed toAllen Byrne2010-06-021-6/+6
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* [svn-r18947] Purpose:Jonathan Kim2010-06-021-6/+22
| | | | | | | | Update Windows testing for h5ls according to the updates for Support follow symbolic links. Description: Sync with hdf5 trunk SVN r18943
* [svn-r18943] Purpose:Jonathan Kim2010-06-0226-218/+842
| | | | | | | | | | | | Support follow symbolic links. Description: Add '--follow-symlinks' option to follow symbolic links (soft and external). Update help page according to RM. Remove some warning messages from compiler. Tested: jam, amani and linew
* [svn-r18942] Allen Byrne2010-06-011-1/+0
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* [svn-r18940] Update Cygwin and Windows referencesAllen Byrne2010-06-012-277/+16
| | | | Removed support for MinGW
* [svn-r18933] Update Cygwin install instructionsAllen Byrne2010-06-011-23/+14
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* [svn-r18930] Enabled mf test since it is fixed.Allen Byrne2010-06-011-2/+1
| | | | Tested: windows
* [svn-r18929] New feature:Albert Cheng2010-06-013-12/+79
| | | | | | | | | | Added ibm-flags to display the IBM XL compilers version information so that configure can report them in the configure summary and the libhdf5.settings file. For now, only the C compiler (xlc) versions are displayed. Also moved the C compiler options setting from ibm-aix to ibm-flags. Tested: NCSA Blue-print, both 32 and 64 bit modes.
* [svn-r18926] Description:Quincey Koziol2010-05-314-93/+67
| | | | | | | | Get down to just one "resize_configs_are_equal" comparison routine. Tested on: Mac OS X/32 10.6.3 (amazon) (too minor to require h5committest)
* [svn-r18925] Updated install of fortran mod filesAllen Byrne2010-05-282-8/+30
| | | | Tested: local linux
* [svn-r18922] Fix for failures for test/mf.c on windows:Vailin Choi2010-05-282-1/+8
| | | | | 1. H5FD_stdio_truncate() windows code: need to do a rewind 2. Make sure fsinfo.fs_addr is initialized before creating the message.
* [svn-r18917] Description:Quincey Koziol2010-05-2732-1404/+1126
| | | | | | | | | | | | | | | | | | | | | | | | Bring r18911 (plus some adaptions to match the code on the trunk) from the metadata journaling "merging" branch to the trunk: More general changes to align trunk with eventual changes from metadata journaling branch. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.3 (amazon) in debug mode Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r18915] Description:Quincey Koziol2010-05-272-24/+28
| | | | | | | | Clean up a couple of compiler warnings (in Windows). Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too minor to require h5committest)
* [svn-r18914] Added fortran library to list of library links.Allen Byrne2010-05-271-9/+9
| | | | Tested: Windows, local linux
* [svn-r18908] Corrected name of cstub libraries (needed to be lowercase)Allen Byrne2010-05-261-5/+5
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* [svn-r18906] Updated with new name of CMake.txtAllen Byrne2010-05-261-1/+1
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* [svn-r18903] Renamed Cmake specific document, making more general for all ↵Allen Byrne2010-05-264-97/+113
| | | | platforms. Updated references in other files.
* [svn-r18898] Added fortran /dbglibs option to fortran compile flags for ↵Allen Byrne2010-05-252-1/+11
| | | | | | windows intel fortran case. Duplicated windows intel fortran flag block for hl/fortran
* [svn-r18894] Purpose: Improve allocation performance of filtered datasets ↵Neil Fortner2010-05-258-74/+95
| | | | | | | | | | | | | with non-default VL fill values. Description: Previously, H5D_chunk_allocate would, if a dataset were filtered and had a non-default VL fill value, allocate a new buffer for every chunk. Changed H5D_chunk_allocate to reuse the existing buffer if possible. Also other miscellaneous cleanup. Tested: jam, linew, amani (h5committest)
* [svn-r18890] Update CMake fortran configure/build with changes from community.Allen Byrne2010-05-255-14/+32
| | | | | | | | - Add an install rule to copy compiled fortran module files - Only build the xlatefile utility if testing and tools are enabled - Don't do MPI HAVE_XXX checks until MPI_FOUND is true - Install needs H5version.h & H5overflow.h to be copied - Add debug information flags to debug compile and link lines for win32 Intel compiler
* [svn-r18885] Add -C {Debug | Release} to ctest command lineAllen Byrne2010-05-241-1/+1
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* [svn-r18882] Maintenance: fixed a typo in email addressElena Pourmal2010-05-221-1/+1
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* [svn-r18881] Maintenance: Fixed a typo in the bug number (should be 1851 ↵Elena Pourmal2010-05-221-1/+1
| | | | instead of 1855)
* [svn-r18880] Bug fix: Elena Pourmal2010-05-223-44/+61
| | | | | | | | Fixed a bug (1855) in H5DSattach_scale, H5DSis_attached and H5DSdetach_scale caused by using H5Tget_native_type function to determine the native type for reading REFERENCE_LIST attribute. The bug was exposed on Mac PPC. Platforms tested: juniper (Mac PPC), jam, amani, linew
* [svn-r18877] Update testh5diff.bat for --follow-symlinks changeAllen Byrne2010-05-211-76/+76
| | | | Tested: windows
* [svn-r18873] Purpose:Jonathan Kim2010-05-2116-143/+143
| | | | | | | | | | | Rename '--follow-links' to '--follow-symlinks' Description: The '--follow-links' option is to follow symbolic links (soft and external). Make the name more intuitive and specific to the feature. Tested: jam, amani and linew
* [svn-r18871] Description:Quincey Koziol2010-05-211-8/+8
| | | | | | | | | Clean up compiler warnings (on Windows, I hope) by marking some routines as taking 'volatile' parameters. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too minor for h5committest)
* [svn-r18868] Purpose: Fix bug in dataset shrinking algorithmNeil Fortner2010-05-204-262/+384
| | | | | | | | | | | | | | | | Description: Previously, it was possible for a chunk to be flushed due to chunk operations in the callback from H5B_iterate in H5D_chunk_prune_by_extent. Because flushing the chunk can force it to be reallocated if it is filtered, this can change the contents of the chunk b-tree in the middle of H5B_iterate. Because H5B_iterate uses a locally cached copy of the b-tree, this causes subsequent operations to be passed incorrect data. Rewrote H5D_chunk_prune_by_extent to avoid H5B_iterate entirely. Also fixed a bug in the dataset expand algorithm that could cause extra chunks to be created. Tested: jam, linew, smirom (h5committest)
* [svn-r18864] Description:Quincey Koziol2010-05-2020-1279/+254
| | | | | | | | | | | | | | | | | | | | General cleanups to align metadata journaling branch and trunk Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.3 (amazon) in debug mode Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r18859] pull r18858 from 185;Allen Byrne2010-05-191-10/+5
| | | | Cange allocation of buffer to use the specified dimensions to calculate the size of a data buffer. Also removed any initialized values.
* [svn-r18856] Added CPack commands for installtion programAllen Byrne2010-05-1918-21/+161
| | | | Tested: local linux and Windows
* [svn-r18837] Description:Quincey Koziol2010-05-1817-1895/+1229
| | | | | | | | | | | | | | | | | | | | | | Remove the size parameter from H5[A]C_unprotect() and the H5[A]C__SIZE_CHANGED_FLAG, switching all clients & tests over to using H5[A]C_resize_entry appropriately. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.3 (amazon) in debug mode Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r18834] Description:Quincey Koziol2010-05-171-1/+2
| | | | | | | | | Correct function enter macro and add 'done' label, for routine that is only invoked when configured with --enable-debug=all. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug & production (too minor to require h5committest)
* [svn-r18832] Description:Quincey Koziol2010-05-171-1/+1
| | | | | | | | Correct error where variable didn't always get initialized correctly. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug & prod Windows w/debug & prod
* [svn-r18831] Purpose:Jonathan Kim2010-05-171-5/+4
| | | | | | | Resolve build issue on Windows due to the location of variable definition. Tested: jam
* [svn-r18827] Description:Quincey Koziol2010-05-171-1/+1
| | | | | | | | Correct error where variable didn't always get initialized correctly. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug & prod Windows w/debug & prod
* [svn-r18823] Snapshot version 1.9 release 69HDF Tester2010-05-1614-28/+28
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* [svn-r18819] Maintenance: fixed typo in a comment line and formatting.Elena Pourmal2010-05-151-5/+5
| | | | Platforms tested: jam (minor fix)
* [svn-r18818] Bug fix: Elena Pourmal2010-05-155-114/+251
| | | | | | | | | | | Fixed a bug in the H5DSdetach_scale function when 0 bytes were allocated after the last reference to a dim. scale was removed from the list of references in a VL element of the DIMENSION_LIST attribute; modified the function to comply with the Spec: DIMENSION_LIST attribute is deleted now when no dimension scales left attached. Platforms tested: jam with electric fence, amani amd linew
* [svn-r18816] Move progname and d_status functions from h5tools to h5tools_utilAllen Byrne2010-05-144-34/+34
| | | | | Tested: linux and windows
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